Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about changes in chromatin accessibility of plants infected by viruses and its potential impact. Here, rice infected by rice stripe virus (RSV) was used to investigate virus‐induced changes in chromatin accessibility. Our analysis identified a total of 6462 open‐ and 3587 closed‐differentially accessible chromatin regions (DACRs) in rice under RSV infection by ATAC‐seq. Additionally, by integrating ATAC‐seq and RNA‐seq, 349 up‐regulated genes in open‐DACRs and 126 down‐regulated genes in closed‐DACRs were identified, of which 34 transcription factors (TFs) were further identified by search of upstream motifs. Transcription levels of eight of these TFs were validated by reverse transcription‐PCR. Importantly, four of these TFs (OsWRKY77, OsWRKY28, OsZFP12 and OsERF91) interacted with RSV proteins and are therefore predicted to play important roles in RSV infection. This is the first application of ATAC‐seq and RNA‐seq techniques to analyse changes in rice chromatin accessibility caused by RSV infection. Integrating ATAC‐seq and RNA‐seq provides a new approach to select candidate TFs in response to virus infection.

中文翻译：

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综合 ATAC-seq 和 RNA-seq 数据分析确定了与水稻条纹病毒感染相关的转录因子

动物研究表明，病毒感染会导致宿主染色质可及性发生变化，但人们对受病毒感染的植物染色质可及性的变化及其潜在影响知之甚少。在这里，使用感染水稻条纹病毒（RSV）的水稻来研究病毒引起的染色质可及性变化。我们的分析通过 ATAC-seq 确定了 RSV 感染下的水稻中总共 6462 个开放式和 3587 个封闭式差异可及染色质区域 (DACR)。此外，通过整合ATAC-seq和RNA-seq，鉴定出了开放DACR中的349个上调基因和封闭DACR中的126个下调基因，其中通过搜索上游基序进一步鉴定了34个转录因子（TF） 。其中八个 TF 的转录水平通过逆转录 PCR 进行了验证。重要的是，其中四个 TF（OsWRKY77、OsWRKY28、OsZFP12 和 OsERF91）与 RSV 蛋白相互作用，因此预计在 RSV 感染中发挥重要作用。这是首次应用ATAC-seq和RNA-seq技术来分析RSV感染引起的水稻染色质可及性的变化。 ATAC-seq 和 RNA-seq 的整合提供了一种选择候选 TF 来应对病毒感染的新方法。